+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-6648 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
タイトル | Ensemble cryo-EM uncovers inchworm-like translocation of a viral IRES through the ribosome | |||||||||
マップデータ | Saccharomyces cerevisiae 80S ribosome bound to eEF2-GDP-sordarin and TSV IRES, Structure I. For classification, 2D masking around the E site was used, including the 5' domain of PKI. | |||||||||
試料 |
| |||||||||
キーワード | cryo-EM / translocation / IRES / ribosome / eEF2 | |||||||||
機能・相同性 | 機能・相同性情報 Peptide chain elongation / Synthesis of diphthamide-EEF2 / positive regulation of translational elongation / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) / negative regulation of glucose mediated signaling pathway / negative regulation of translational frameshifting / Negative regulators of DDX58/IFIH1 signaling / positive regulation of translational fidelity / Protein methylation / RMTs methylate histone arginines ...Peptide chain elongation / Synthesis of diphthamide-EEF2 / positive regulation of translational elongation / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) / negative regulation of glucose mediated signaling pathway / negative regulation of translational frameshifting / Negative regulators of DDX58/IFIH1 signaling / positive regulation of translational fidelity / Protein methylation / RMTs methylate histone arginines / mTORC1-mediated signalling / Protein hydroxylation / ribosome-associated ubiquitin-dependent protein catabolic process / GDP-dissociation inhibitor activity / nonfunctional rRNA decay / pre-mRNA 5'-splice site binding / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / Ribosomal scanning and start codon recognition / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / preribosome, small subunit precursor / response to cycloheximide / mRNA destabilization / Major pathway of rRNA processing in the nucleolus and cytosol / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / Formation of a pool of free 40S subunits / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / negative regulation of mRNA splicing, via spliceosome / L13a-mediated translational silencing of Ceruloplasmin expression / regulation of cellular amino acid metabolic process / preribosome, large subunit precursor / translational elongation / ribosomal large subunit export from nucleus / G-protein alpha-subunit binding / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 90S preribosome / positive regulation of protein kinase activity / protein-RNA complex assembly / regulation of translational fidelity / Ub-specific processing proteases / translation elongation factor activity / ribosomal subunit export from nucleus / translation regulator activity / ribosomal small subunit export from nucleus / translational termination / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / DNA-(apurinic or apyrimidinic site) endonuclease activity / Neutrophil degranulation / maturation of LSU-rRNA / cellular response to amino acid starvation / rescue of stalled ribosome / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosome assembly / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / maturation of SSU-rRNA / small-subunit processome / translational initiation / macroautophagy / protein kinase C binding / 加水分解酵素; 酸無水物に作用; GTPに作用・細胞または細胞小器官の運動に関与 / maintenance of translational fidelity / modification-dependent protein catabolic process / cytoplasmic stress granule / rRNA processing / protein tag activity / ribosome biogenesis / ribosome binding / ribosomal small subunit biogenesis / ribosomal small subunit assembly / protein-folding chaperone binding / small ribosomal subunit / small ribosomal subunit rRNA binding / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / rRNA binding / negative regulation of translation / ribosome / protein ubiquitination / structural constituent of ribosome / translation / positive regulation of protein phosphorylation / ribonucleoprotein complex / G protein-coupled receptor signaling pathway / negative regulation of gene expression / response to antibiotic / GTPase activity / mRNA binding / ubiquitin protein ligase binding / nucleolus / GTP binding / mitochondrion / RNA binding / zinc ion binding 類似検索 - 分子機能 | |||||||||
生物種 | Saccharomyces cerevisiae (パン酵母) / Taura syndrome virus (ウイルス) | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 4.0 Å | |||||||||
データ登録者 | Abeyrathne PD / Koh CS / Grant T / Grigorieff N / Korostelev AA | |||||||||
引用 | ジャーナル: Elife / 年: 2016 タイトル: Ensemble cryo-EM uncovers inchworm-like translocation of a viral IRES through the ribosome. 著者: Priyanka D Abeyrathne / Cha San Koh / Timothy Grant / Nikolaus Grigorieff / Andrei A Korostelev / 要旨: Internal ribosome entry sites (IRESs) mediate cap-independent translation of viral mRNAs. Using electron cryo-microscopy of a single specimen, we present five ribosome structures formed with the ...Internal ribosome entry sites (IRESs) mediate cap-independent translation of viral mRNAs. Using electron cryo-microscopy of a single specimen, we present five ribosome structures formed with the Taura syndrome virus IRES and translocase eEF2•GTP bound with sordarin. The structures suggest a trajectory of IRES translocation, required for translation initiation, and provide an unprecedented view of eEF2 dynamics. The IRES rearranges from extended to bent to extended conformations. This inchworm-like movement is coupled with ribosomal inter-subunit rotation and 40S head swivel. eEF2, attached to the 60S subunit, slides along the rotating 40S subunit to enter the A site. Its diphthamide-bearing tip at domain IV separates the tRNA-mRNA-like pseudoknot I (PKI) of the IRES from the decoding center. This unlocks 40S domains, facilitating head swivel and biasing IRES translocation via hitherto-elusive intermediates with PKI captured between the A and P sites. The structures suggest missing links in our understanding of tRNA translocation. | |||||||||
履歴 |
|
-構造の表示
ムービー |
ムービービューア |
---|---|
構造ビューア | EMマップ: SurfViewMolmilJmol/JSmol |
添付画像 |
-ダウンロードとリンク
-EMDBアーカイブ
マップデータ | emd_6648.map.gz | 21.4 MB | EMDBマップデータ形式 | |
---|---|---|---|---|
ヘッダ (付随情報) | emd-6648-v30.xml emd-6648.xml | 11.6 KB 11.6 KB | 表示 表示 | EMDBヘッダ |
画像 | 400_6648.gif 80_6648.gif | 84.8 KB 4.7 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-6648 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6648 | HTTPS FTP |
-関連構造データ
関連構造データ | 5juoMC 6643C 6644C 6645C 6646C 6647C 6649C 6650C 6651C 6652C 6653C 5jupC 5jusC 5jutC 5juuC M: このマップから作成された原子モデル C: 同じ文献を引用 (文献) |
---|---|
類似構造データ |
-リンク
EMDBのページ | EMDB (EBI/PDBe) / EMDataResource |
---|---|
「今月の分子」の関連する項目 |
-マップ
ファイル | ダウンロード / ファイル: emd_6648.map.gz / 形式: CCP4 / 大きさ: 62.5 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
注釈 | Saccharomyces cerevisiae 80S ribosome bound to eEF2-GDP-sordarin and TSV IRES, Structure I. For classification, 2D masking around the E site was used, including the 5' domain of PKI. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.64 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
密度 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
対称性 | 空間群: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
詳細 | EMDB XML:
CCP4マップ ヘッダ情報:
|
-添付データ
-試料の構成要素
-全体 : Saccharomyces cerevisiae 80S ribosome bound to TSV IRES and eEF2 ...
全体 | 名称: Saccharomyces cerevisiae 80S ribosome bound to TSV IRES and eEF2 translation initiation complex, Structure I, Map 2 |
---|---|
要素 |
|
-超分子 #1000: Saccharomyces cerevisiae 80S ribosome bound to TSV IRES and eEF2 ...
超分子 | 名称: Saccharomyces cerevisiae 80S ribosome bound to TSV IRES and eEF2 translation initiation complex, Structure I, Map 2 タイプ: sample / ID: 1000 / Number unique components: 3 |
---|---|
分子量 | 理論値: 3.2 MDa |
-超分子 #1: Ribosome
超分子 | 名称: Ribosome / タイプ: complex / ID: 1 / 組換発現: No / データベース: NCBI / Ribosome-details: ribosome-eukaryote: ALL |
---|---|
由来(天然) | 生物種: Saccharomyces cerevisiae (パン酵母) / 別称: Yeast |
分子量 | 理論値: 3.2 MDa |
-分子 #1: Internal Ribosome Entry Site
分子 | 名称: Internal Ribosome Entry Site / タイプ: rna / ID: 1 / Name.synonym: IRES / 分類: OTHER / Structure: SINGLE STRANDED / Synthetic?: Yes |
---|---|
由来(天然) | 生物種: Taura syndrome virus (ウイルス) |
分子量 | 理論値: 80 KDa |
-分子 #2: eukaryotic elongation factor 2
分子 | 名称: eukaryotic elongation factor 2 / タイプ: protein_or_peptide / ID: 2 / Name.synonym: eEF2 / 組換発現: No / データベース: NCBI |
---|---|
由来(天然) | 生物種: Saccharomyces cerevisiae (パン酵母) / 別称: Yeast |
分子量 | 理論値: 94 KDa |
-実験情報
-構造解析
手法 | クライオ電子顕微鏡法 |
---|---|
解析 | 単粒子再構成法 |
試料の集合状態 | particle |
-試料調製
濃度 | 0.3 mg/mL |
---|---|
グリッド | 詳細: Quantifoil Cu 200 mesh |
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 85 % / チャンバー内温度: 103 K / 装置: FEI VITROBOT MARK II |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
---|---|
アライメント法 | Legacy - 非点収差: Objective lens astigmatism was corrected at 120,000 times magnification. Legacy - Electron beam tilt params: 0.7 |
詳細 | 10 electrons/physical pixel/second |
日付 | 2015年11月11日 |
撮影 | カテゴリ: CCD フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k) デジタル化 - サンプリング間隔: 5 µm / 実像数: 2662 / 平均電子線量: 70 e/Å2 / 詳細: Images recorded as movies in super-resolution mode. / ビット/ピクセル: 8 |
電子線 | 加速電圧: 300 kV / 電子線源: FIELD EMISSION GUN |
電子光学系 | 倍率(補正後): 30487 / 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD / Cs: 2.7 mm / 最大 デフォーカス(公称値): 2.5 µm / 最小 デフォーカス(公称値): 0.7 µm / 倍率(公称値): 18000 |
試料ステージ | 試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
-画像解析
詳細 | FREALIGN |
---|---|
CTF補正 | 詳細: each particle |
最終 再構成 | アルゴリズム: OTHER / 解像度のタイプ: BY AUTHOR / 解像度: 4.0 Å / 解像度の算出法: OTHER / ソフトウェア - 名称: Unblur, CTFFIND4, FREALIGN 詳細: The highest resolution included in the refinement was 7 Angstrom. 使用した粒子像数: 1105737 |